|
| Status |
Public on Oct 01, 2015 |
| Title |
Rtf1_KD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa cells
genotype: Rtf1 knockdown
|
| Treatment protocol |
HeLa cells were infected with recombinant lentivirus expressing no shRNA or expressing one of functionally validated shRNAs and selected in the presence of 5 µg/ml Blasticidin for pLenti6-based vectors or 1 µg/ml Puromycin for pRSI9-based vectors.
|
| Growth protocol |
DMEM+10%FCS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared at 4 or 7 days post-infection using the AGPC method.
Following the removal of rRNA using the RiboMinus Eukaryote Kit (Life Technologies), libraries were constructed using the Ion Total RNA-Seq Kit (Life Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Rtf1 knockdown: replicate 2
|
| Data processing |
Basecalling and trimming of adaptor sequence were performed using Torrent Suite Software.
Sequenced reads were mapped to the human genome GRch37.p9 and reads per kilobase of transcript per million reads mapped (RPKMs) were calculated using CLC Genomics Workbench 6.5.1 with default settings.
Genome_build: GRch37.p9
Supplementary_files_format_and_content: an Excel file including RPKM values for all the samples
|
| |
|
| Submission date |
Sep 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuki Yamaguchi |
| E-mail(s) |
yyamaguc@bio.titech.ac.jp
|
| Organization name |
Tokyo Institute of Technology
|
| Department |
Life Science and Technology
|
| Street address |
4259 Nagatsuta
|
| City |
Yokohama |
| ZIP/Postal code |
226-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE73632 |
Comparative analysis of Rtf1- and PAF1C-regulated genes |
|
| Relations |
| BioSample |
SAMN04123927 |
| SRA |
SRX1297545 |
